A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
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DOI：
10.1186/1471-2229-10-55
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发表时间：
2010-03-30
影响因子：
5.3
通讯作者：
Shirasu K
中科院分区：
文献类型：
--
作者：
Yoshida S;Ishida JK;Kamal NM;Ali AM;Namba S;Shirasu K
专性寄生植物独脚金（Striga hermonthica）感染主要谷物作物，如高粱、玉米和小米，是非洲最具破坏性的杂草害虫。对其寄生性质的了解将有助于发展更复杂的管理方法。然而，目前可供其研究的分子和基因组资源是有限的。我们构建了一个完整的hermonthica cDNA文库，测序了37710个克隆，获得了67814个EST序列。est被组装成17,317个单基因，其中包括10,319个contigs和6,818个singleton。将该单基因数据集与其他植物基因组或est进行比较分析。在拟南芥、杨树和葡萄等其他双子叶植物中，约80%的单基因具有同源性。我们发现，在半寄生三绒藻中有589个单基因是保守的，而在其他植物中没有。这些都是很好的候选基因，专门参与植物寄生。此外，我们还发现了1445个假定的简单序列重复序列（SSRs）。我们测试了64对ssr侧翼的PCR引物，以开发检测多态性的遗传标记。多数引物组扩增的多态带均来自同一地点采集的单株植物，表明该植物具有较高的遗传多样性。选取10对引物，对不同寄主种类和地理位置的田间收获的红月牙进行分析。聚类分析表明遗传距离与宿主特异性无关。我们的数据提供了第一个广泛的分子资源，包括EST序列，与其他植物基因组的比较分析，以及有用的遗传标记。所有的数据都存储在一个基于网络的数据库中，可以免费使用。这些资源将有助于基因组注释、基因发现、功能分析、分子育种、流行病学研究和植物进化研究。
The obligate parasitic plant witchweed (Striga hermonthica) infects major cereal crops such as sorghum, maize, and millet, and is the most devastating weed pest in Africa. An understanding of the nature of its parasitism would contribute to the development of more sophisticated management methods. However, the molecular and genomic resources currently available for the study of S. hermonthica are limited. We constructed a full-length enriched cDNA library of S. hermonthica, sequenced 37,710 clones from the library, and obtained 67,814 expressed sequence tag (EST) sequences. The ESTs were assembled into 17,317 unigenes that included 10,319 contigs and 6,818 singletons. The S. hermonthica unigene dataset was subjected to a comparative analysis with other plant genomes or ESTs. Approximately 80% of the unigenes have homologs in other dicotyledonous plants including Arabidopsis, poplar, and grape. We found that 589 unigenes are conserved in the hemiparasitic Triphysaria species but not in other plant species. These are good candidates for genes specifically involved in plant parasitism. Furthermore, we found 1,445 putative simple sequence repeats (SSRs) in the S. hermonthica unigene dataset. We tested 64 pairs of PCR primers flanking the SSRs to develop genetic markers for the detection of polymorphisms. Most primer sets amplified polymorphicbands from individual plants collected at a single location, indicating high genetic diversity in S. hermonthica. We selected 10 primer pairs to analyze S. hermonthica harvested in the field from different host species and geographic locations. A clustering analysis suggests that genetic distances are not correlated with host specificity. Our data provide the first extensive set of molecular resources for studying S. hermonthica, and include EST sequences, a comparative analysis with other plant genomes, and useful genetic markers. All the data are stored in a web-based database and freely available. These resources will be useful for genome annotation, gene discovery, functional analysis, molecular breeding, epidemiological studies, and studies of plant evolution.
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